On Wed, Jan 16, 2013 at 7:28 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>> Renaming the file to replace the colon with (say) an underscore allows
>> a manual qsub to work fine with UGE. I've edited Galaxy to avoid the
>> colons (patch below) but the submission still fails.
>>

Hi Peter,
After seeing your email I now wonder if the problem I described
here[1] and didn't get any answer about it is related to your findings
while trying UGE.
[1]http://dev.list.galaxyproject.org/Issue-when-enabling-use-tasked-jobs-with-torque-and-nfs-td4657294.html
I noticed the only mayor different I can notice between jobs
submission with and without tasked option enabled is a colon in the
name. See the relevant output from "qstat -f JOBID" below.
Without tasked:
Error_Path =
/local/opt/galaxy/galaxy-dist.torque/database/job_working_directory/000/34/34.drmerr
Output_Path =
/local/opt/galaxy/galaxy-dist.torque/database/job_working_directory/000/34/34.drmout
Job finishes and galaxy is able to collect drmerr and drmout files.
With tasked:
Error_Path =
/local/opt/galaxy/galaxy-dist.torque/database/job_working_directory/000/33/task_4/33:30.drmerr
Output_Path =
/local/opt/galaxy/galaxy-dist.torque/database/job_working_directory/000/33/task_4/33:30.drmout
sched_hint = Post job file processing error; job 40.head.local on host
node01.local/7+node01.local/6+node01.local/5+node01.local/4+node01.local/3+node01.local/2+node01.local/1+node01.brel.local/0
Unable to copy file /var/spool/torque/spool/40.head.local.OU to
galaxy@/local/opt/galaxy/galaxy-dist.torque/database/job_working_directory/000/33/task_4/33:30.drmout
*** error from copy
cp: cannot create regular file
`galaxy@/local/opt/galaxy/galaxy-dist.torque/database/job_working_directory/000/33/task_4/33:30.drmout':
No such file or directory
*** end error output
Output retained on that host in: /var/spool/torque/undelivered/40.head.local.OU
Unable to copy file /var/spool/torque/spool/40.head.local.ER to
galaxy@/local/opt/galaxy/galaxy-dist.torque/database/job_working_directory/000/33/task_4/33:30.drmerr
*** error from copy
cp: cannot create regular file
`galaxy@/local/opt/galaxy/galaxy-dist.torque/database/job_working_directory/000/33/task_4/33:30.drmerr':
No such file or directory
*** end error output
Output retained on that host in: /var/spool/torque/undelivered/40.head.local.ER
Job finishes, galaxy is not able to collect drmerr and drmout files
and job turns green in the history panels but includes partial
information about not being able to collect drmerr and drmout files.
I will try to see if switching from using colon to underscore could
help in this situation also. Although I'm also worry about "galaxy@"
in the file path. I don't understand why is there.
I'm using latest Galaxy Dist, Torque 4.1.4, Maui 3.3.1 and pbs-drmaa
1.0.12. I tried using pbs-python but that failed for me. I also tried
libdrmaa from this Torque version with the same exact results.
Best,
Carlos
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